To understand temperature structure or magma distribution in the crust and uppermost mantle, it is essential to know their attenuation structure. This study estimated the 3-D S-wave attenuation structure in the crust and uppermost mantle at the northern Izu–Bonin arc, taking into account the apparent attenuation due to multiple forward scattering. In the uppermost mantle, two areas of high seismic attenuation (high Q −1) imaged beneath the volcanic front were mostly colocated with low-velocity anomalies. This coincidence suggests that these high-Q −1 areas in low-velocity zones are the most likely candidates for high-temperature regions beneath volcanoes. The distribution of random inhomogeneities indicated the presence of three anomalies beneath the volcanic front: Two were in high-Q −1 areas but the third was in a moderate-Q −1 area, indicating a low correlation between random inhomogeneities and Q −1. All three anomalies of random inhomogeneities were rich in short-wavelength spectra. The most probable interpretation of such spectra is the presence of volcanic rock, which would be related to accumulated magma intrusion during episodes of volcanic activity. Therefore, the different distributions of Q −1 and random inhomogeneities imply that the positions of hot regions in the uppermost mantle beneath this arc have changed temporally; therefore, they may provide important constraints on the evolutionary processes of arc crust and volcanoes.